Contacts of the helix formed by residues 316 - 331 (chain D) in PDB entry 3OP5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 316 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A GLU* 3.5 36.3 - - + +
32B MET* 3.4 46.4 - - + +
33B ALA* 4.1 13.0 - - + +
305D THR* 5.8 0.4 - - + +
309D LEU* 5.1 2.2 - - - +
314D LYS 3.7 4.0 + - - +
315D PRO* 1.3 70.2 - - - +
317D TYR* 1.4 63.3 - - - +
318D GLU* 3.3 4.9 - - + -
319D ASN* 3.2 24.5 + - + +
320D LEU* 3.3 16.4 + - - +
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Residues in contact with TYR 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A GLU* 5.3 1.3 + - - -
162D LEU* 4.5 10.2 - - + +
165D LEU* 5.1 0.2 - - + -
166D GLU* 3.7 61.5 - - + +
169D HIS* 2.7 43.8 + + + +
170D GLU* 4.6 8.9 + - - -
240D ARG* 3.5 2.6 + - - -
244D LEU* 4.7 13.7 - - + -
314D LYS* 4.6 11.9 - - + -
315D PRO* 3.2 53.6 + - + +
316D LEU* 1.4 69.9 - - - +
318D GLU* 1.3 57.6 + - - +
320D LEU* 3.3 12.5 + - + +
321D ARG* 3.0 37.3 + - - +
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Residues in contact with GLU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLU* 4.6 4.0 - - - +
316D LEU* 3.3 2.8 - - + -
317D TYR* 1.3 78.0 - - - +
319D ASN* 1.3 56.3 - - - +
321D ARG* 2.9 39.6 + - - +
322D ASP* 3.0 40.8 + - - +
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Residues in contact with ASN 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B MET* 3.6 50.1 - - - +
305D THR* 3.5 30.9 + - - +
316D LEU* 3.2 17.1 + - + +
318D GLU* 1.3 77.4 - - - +
320D LEU* 1.3 61.3 + - - +
322D ASP* 3.4 13.4 + - - +
323D ILE* 3.2 30.5 + - - +
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LEU* 3.9 18.2 - - + -
244D LEU* 3.7 38.1 - - + -
302D TYR* 3.7 26.3 - - + +
305D THR* 3.9 33.2 - - + -
306D VAL* 4.2 9.0 - - + -
309D LEU* 5.7 1.1 - - + -
315D PRO* 4.6 5.2 - - + -
316D LEU 3.3 13.2 + - - +
317D TYR* 3.3 15.0 + - + +
319D ASN* 1.3 73.3 - - - +
321D ARG* 1.3 64.5 + - - +
323D ILE* 3.4 11.3 + - + +
324D LEU* 3.3 26.0 + - - +
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Residues in contact with ARG 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D LEU* 3.8 23.8 + - + +
160D ARG* 6.2 0.7 - - - +
162D LEU* 3.5 35.9 + - + +
163D ASP* 3.1 31.0 + - - +
166D GLU* 2.6 29.7 + - - +
317D TYR* 3.0 24.5 + - - +
318D GLU* 2.9 50.3 + - - +
320D LEU* 1.3 73.4 - - - +
322D ASP* 1.4 53.6 + - - +
324D LEU* 3.2 4.2 + - - +
325D LEU* 2.8 47.1 + - + +
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Residues in contact with ASP 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D GLU* 3.0 30.1 + - - +
319D ASN* 3.4 13.8 + - - +
321D ARG* 1.4 71.1 - - - +
323D ILE* 1.4 60.6 + - - +
325D LEU* 3.7 17.5 - - - +
326D GLN* 2.9 38.2 + - + +
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Residues in contact with ILE 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 4.8 7.0 - - + -
298D GLU* 3.3 43.3 - - + +
301D LYS* 3.9 23.3 - - + +
302D TYR* 3.8 14.6 - - + +
305D THR* 3.4 30.1 - - - +
319D ASN* 3.2 26.7 + - - +
320D LEU* 3.5 15.5 - - - +
321D ARG 3.3 0.2 - - - -
322D ASP* 1.4 74.8 - - + +
324D LEU* 1.3 62.3 + - + +
326D GLN* 3.3 25.1 + - - +
327D GLY 3.4 2.6 + - - -
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Residues in contact with LEU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LEU* 3.6 32.4 - - + +
158D SER* 3.6 31.4 - - - -
159D LEU* 3.9 14.6 - - + +
162D LEU* 3.7 27.4 - - + -
251D MET* 4.2 19.7 - - + -
298D GLU* 4.6 8.3 - - + -
299D ILE* 5.2 0.9 - - + -
302D TYR* 4.4 18.2 - - + -
320D LEU 3.3 8.9 + - - +
321D ARG 3.2 7.2 + - - +
323D ILE* 1.3 76.2 - - + +
325D LEU* 1.4 64.4 + - - +
327D GLY* 3.2 11.1 + - - -
328D LEU* 3.2 15.2 + - - +
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Residues in contact with LEU 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D LEU* 4.0 15.7 - - + -
321D ARG* 2.8 32.2 + - + +
322D ASP* 3.3 18.4 + - - +
324D LEU* 1.4 73.0 - - - +
326D GLN* 1.4 59.9 + - - +
328D LEU* 3.3 11.5 + - + +
329D LYS* 3.1 25.8 + - - +
335D ASP* 3.7 34.5 - - + +
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Residues in contact with GLN 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ASP* 5.1 3.8 + - - -
298D GLU* 5.7 0.7 - - + -
301D LYS* 3.8 25.3 + - - +
322D ASP* 2.9 21.0 + - + +
323D ILE* 3.5 19.0 - - - +
325D LEU* 1.4 73.4 - - + +
327D GLY* 1.3 59.6 - - - +
329D LYS* 3.4 12.6 + - + +
330D ALA* 3.0 28.5 + - - +
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Residues in contact with GLY 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ARG* 4.3 0.9 + - - -
155D LEU* 3.7 8.3 - - - +
298D GLU* 3.7 31.8 - - - +
323D ILE 3.4 4.4 + - - -
324D LEU 3.2 9.4 + - - -
326D GLN* 1.3 79.1 - - - +
328D LEU* 1.4 58.5 + - - +
330D ALA* 3.4 8.4 + - - +
331D ILE* 3.3 27.0 + - - +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LYS* 4.0 23.3 - - + +
155D LEU* 3.9 23.6 - - + -
156D GLN* 3.6 26.7 - - - +
159D LEU* 3.7 27.4 - - + -
324D LEU 3.2 11.7 + - - +
325D LEU* 3.3 15.9 + - + +
327D GLY* 1.4 71.5 - - - +
329D LYS* 1.3 58.2 + - - +
331D ILE* 3.3 14.7 - - + +
333D SER* 2.8 34.7 + - - -
334D LYS* 4.3 12.3 - - - +
335D ASP* 3.8 14.8 - - - +
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Residues in contact with LYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D LEU 3.1 12.5 + - - +
326D GLN* 3.4 14.3 + - + +
328D LEU* 1.3 74.5 - - - +
330D ALA* 1.4 62.8 + - - +
332D GLY* 3.1 13.9 + - - -
333D SER 3.8 8.7 + - - +
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Residues in contact with ALA 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ARG* 4.1 17.7 - - - +
326D GLN 3.0 14.4 + - - +
327D GLY* 3.4 11.9 - - - +
328D LEU 3.3 0.4 - - - -
329D LYS* 1.4 76.8 - - - +
331D ILE* 1.4 56.5 + - - +
332D GLY 3.3 2.4 + - - -
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Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ARG* 3.6 46.4 - - + +
152D LYS* 3.8 40.4 - - + +
155D LEU* 4.8 2.0 - - + -
327D GLY 3.3 8.5 + - - +
328D LEU* 3.3 19.1 - - + +
330D ALA* 1.4 74.8 - - - +
332D GLY* 1.3 60.1 + - - +
333D SER* 3.5 15.8 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il